Journal of Molecular Modeling最新文献

{"title":"Theoretical characterizations on three oxygen-containing polyatomic anion binding of the single/double pincer-like receptors","authors":"Pei Zhao,&nbsp;Qingqing Yao,&nbsp;Yue Li,&nbsp;Wenbo Zhang,&nbsp;Yanzhi Liu,&nbsp;Zhi-Feng Li,&nbsp;Kun Yuan","doi":"10.1007/s00894-026-06964-5","DOIUrl":"10.1007/s00894-026-06964-5","url":null,"abstract":"<div><h3>Context</h3><p>In this paper, density functional theory calculations were used to systematically characterize the binding behavior of the two types of pincer-like receptors with different configurations (E-type and Z-type) to three oxygen-containing polyatomic anions (SO₄²⁻, C₂O₄²⁻ and NO₃⁻). The E-type receptor (2ENH₂) shows slightly preferential binding of SO₄²⁻. Independent gradient model based on Hirshfeld partition (IGMH) analysis characterized the non-covalent interaction patterns between the receptor and anion. Meanwhile, molecular electrostatic potential (ESP) analysis revealed changes in charge distribution upon anion binding. UV–Vis spectra and ¹H NMR calculations provided complementary information on the electronic and structural changes induced by complexation between anion and receptor. In addition, ab initio molecular dynamics (AIMD) simulations were used to examine the structural persistence of representative host–guest complexes. Overall, the results clarify how receptor configuration, hydrogen-bonding topology, anion properties, and solvent environment collectively influence anion recognition.</p><h3>Methods</h3><p>All geometries were optimized at the B3LYP-D3BJ/def2-SVP level of theory without any symmetry constraints. The host–guest binding energies (Δ<i>E</i>_b^cp) were corrected for basis set superposition error (BSSE). Additional calculations using B3LYP-D3BJ/def2-TZVP with counterpoise correction were performed for selected complexes to assess the robustness of the binding energies. Wave function analyses were performed using the Multiwfn program. AIMD simulations were using the ORCA 5.0 program with the composite method of B97-3c developed by Grimme and coworkers. All other calculations were performed using the Gaussian 16 program.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Substituent‑controlled energy‑sensitivity trade‑off in (E)-1,2-bis(tetrazolo[1,5-d][1,2,3,4]tetrazin-7(1H)-yl)diazene derivatives","authors":"Chao Zhang,&nbsp;Xiaowei Wu,&nbsp;Liqun Sun,&nbsp;Congguang Zhang","doi":"10.1007/s00894-026-06965-4","DOIUrl":"10.1007/s00894-026-06965-4","url":null,"abstract":"<div><h3>Context</h3><p>A series of (<i>E</i>)-1,2-bis(tetrazolo[1,5‑<i>d</i>][1,2,3,4]tetrazin-7(1<i>H</i>)-yl)diazene derivatives featuring extended nitrogen chains with 16–22 consecutive nitrogen atoms were designed and computationally assessed for both energetic characteristics and safety performances. Two nitro‑containing compounds, (<i>E</i>)-1,2-bis(1-nitrotetrazolo[1,5-<i>d</i>][1,2,3,4]tetrazin-7(1<i>H</i>)-yl)diazene (B2) and (<i>E</i>)-<i>N</i>-(7-((1-nitrotetrazolo[1,5-<i>d</i>][1,2,3,4]tetrazin-7(1<i>H</i>)-yl)diazenyl)tetrazolo[1,5-<i>d</i>][1,2,3,4]tetrazin-1(7<i>H</i>)-yl)nitramide (C3), with densities exceeding RDX, detonation velocities exceeding CL-20, detonation pressures close to CL-20, and predicted sensitivities lower than RDX, HMX, and CL-20, thus emerging as particularly promising high-energy low-sensitivity candidates. Frontier orbital analysis reveals that the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are primarily localized on the central skeleton, implicating this core in electronic transitions. Substituent groups narrow the HOMO-LUMO gap, and electrostatic potential maps indicate strongly polarized charge distributions. The energetic contribution of substituents follows the order of -NO₂ &gt; -NHNO₂ &gt; -N₃ &gt; -NH₂ &gt; -NHNH₂, with the safety ranking being exactly the reverse. Collectively, this work provides a novel and viable strategy for the rational design of insensitive high‑energy materials with long catenated nitrogen chains.</p><h3>Methods</h3><p>Full geometry optimizations of all compounds were performed by B3LYP functional and 6-311G** basis set under DFT, as implemented by Gaussian 09 package. The enthalpy of formation of all compounds was derived from both isodesmic and atomization reaction paths. The detonation characteristics of these compounds were obtained by the Kamlet-Jacobs (K-J) equations, and the safety performance of these compounds was evaluated by impact sensitivity, which is measured by <i>h</i>₅₀ value.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-atom lithium adsorption-induced electronic and optical modulation in armchair graphene nanoribbons: a PBE and screened-hybrid DFT study","authors":"Yuzhi Yan","doi":"10.1007/s00894-026-06953-8","DOIUrl":"10.1007/s00894-026-06953-8","url":null,"abstract":"<div><h3>Context</h3><p>Lithium adsorption can alter the electronic and optical response of graphene nanoribbons, but earlier studies have generally treated adsorption stability, electronic structure, and optical spectra separately. The present analysis links adsorption-site energetics and charge transfer to the width-dependent electronic and optical response of hydrogen-terminated armchair graphene nanoribbons.</p><h3>Results</h3><p>The hollow site was lowest in energy, with adsorption energies of − 1.32 and − 1.25 eV and Li-to-ribbon charge transfers of 0.86 and 0.84 electron for widths 6 and 8, respectively. PBE band gaps of 0.78 and 0.11 eV increased to 1.23 and 0.24 eV under the screened-hybrid benchmark, whereas Li adsorption produced bands crossing the Fermi level under both treatments. The first longitudinal absorption peak shifted from 1.70 to 0.90 eV for width 6 (red shift) but from 0.30 to 1.10 eV for width 8 (blue shift). The previously reported static longitudinal refractive index of 21.02 was identified as a transcription error and corrected to 2.10.</p><h3>Conclusions</h3><p>Within the independent-particle approximation, Li adsorption produces a robust donor-induced metallic response, while the direction and magnitude of the optical shift remain width-family dependent. These results support further experimental and many-body validation rather than direct device-level claims.</p><h3>Methods</h3><p>Full-potential DFT calculations were performed with WIEN2k using PBE-GGA, explicit structural relaxation, site-resolved adsorption energies, charge-density-difference and electron-localization analyses, band structures, orbital-projected density of states, and polarization-resolved optical functions. Widths 5–10 and a concentration series were evaluated, and representative width-6 and width-8 structures were benchmarked with the WIEN2k screened-hybrid implementation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ethyl substitution enhances field-induced polarization in selenols and lowers the C–Se bond dissociation threshold","authors":"Pengjun Tang,&nbsp;Siwei Qiu,&nbsp;Yuzhu Liu","doi":"10.1007/s00894-026-06961-8","DOIUrl":"10.1007/s00894-026-06961-8","url":null,"abstract":"<div><h3>Context</h3><p>Alkyl substitution may alter the polarization and bond-selective dissociation of selenols in oriented external electric fields. We compare methaneselenol (CH₃SeH) and ethaneselenol (C₂H₅SeH) to determine how replacing methyl with ethyl affects their structural, electronic, spectroscopic, and dissociation responses. Increasing the field strength elongates the C–Se bond, increases the dipole moment, and generally narrows the frontier-orbital energy gap in both molecules. Changes in C–Se–related infrared bands, red shifts of ultraviolet–visible absorption, and lower excitation energies indicate field-induced electronic redistribution and bond weakening. These responses are more pronounced for C₂H₅SeH. Potential-energy scans show preferential promotion of C–Se cleavage, whereas Se–H cleavage is affected less strongly. The magnitude of the fitted slope of the C–Se scan barrier versus field strength is approximately 21.5% greater for C₂H₅SeH. Linear extrapolation to a zero scan barrier gives critical fields of approximately 26.8 and 20.5 V nm⁻¹ for CH₃SeH and C₂H₅SeH, respectively, a reduction of approximately 23.5%. These extrapolated values suggest that ethyl substitution enhances field-induced polarization and lowers the C–Se dissociation threshold.</p><h3>Methods</h3><p> Geometry optimizations, vibrational analyses, and TD-DFT calculations were performed using Gaussian 16 at the B3PW91/6-311+G(d,p) level. Structural, electronic, and spectroscopic responses were examined over 0–15.43 V nm⁻¹. Single-point potential-energy scans at zero and finite fields were combined with estimates of tunneling ionization rates and mean ionization times.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Modeling and MM-PBSA-Based Molecular Dynamics Investigation of Unexplored tRNA Isoleucine Lysidine Synthetase from Mycobacterium tuberculosis with Hyperbranched Amoxicilloyl-Poly-L-Lysine","authors":"Priyanka Nath,&nbsp;Bipasha Choudhury,&nbsp;Saquib Ahmed M. A. Peerzade,&nbsp;Arun Goyal,&nbsp;Shreyas Bapat","doi":"10.1007/s00894-026-06925-y","DOIUrl":"10.1007/s00894-026-06925-y","url":null,"abstract":"<div><h3>Context</h3><p>Integrated <i>in-</i>silico approach employed to characterize tRNA isoleucine lysidine synthetase enzyme (<i>Mt</i>TilS; UniProt P9WG52), which is essential for protein synthesis in <i>Mycobacterium tuberculosis</i> and to design Amoxicilloyl-Poly-L-Lysine (APL) compounds as putative inhibitors. <i>Mt</i>TilS (323 aa) contained TilS (9–230), substrate-binding (249–323) domains and conserved SGGXDS motif. Homology modeling revealed Rossmann-like α/β/α fold, favourable validation (ERRAT 96%, VERIFY3D 81.8%, ProSA − 9.96) and positively charged N-terminal groove (druggability ~ 0.8). APL compounds showed predicted antibacterial activity, high aqueous solubility and low predicted toxicity. Docking prioritized APL-3 (− 7.0 kcal/mol) as favourable inhibitor. Three independent 200 ns molecular dynamics simulations showed preservation of protein fold and ligand association. Cluster analysis indicated convergence toward dominant conformational states. Principal component analysis (PCA) showed broader but reproducible conformational sampling. Free energy landscape (FEL) analysis identified low-energy conformational basins. Dynamic cross-correlation matrix (DCCM) analysis showed conserved correlated residue motions. MM-PBSA indicated favourable binding free energy (-60.0 ± 24.6 kJ/mol) with van der Waals and electrostatic interactions as major contributors while Arg101, Met145, Tyr105, Arg146, Arg140 and Arg219 as major energetic contributors. Preliminary computational evidence supporting <i>Mt</i>TilS as target and APL-3 as putative inhibitor candidate necessitating further experimental validation.</p><h3>Methods</h3><p><i>Mt</i>TilS sequence analyzed using CDD, BLAST and MEGA-X. Structure modeled with Phyre2 minimized using Swiss-PDB Viewer/GROMOS96, validated with SAVES-6.0 and visualized in PyMOL-2.0. Binding pockets and druggability predicted using HDOCK and DoGSiteScorer. APL designed in Avogadro (MMFF94) and screened using AntiBac-Pred. ADME/toxicity assessed using SwissADME and ProTox-II. Docking performed with AutoDock Vina-1.2.0 and MD using GROMACS (CHARMM36ff). Trajectories analyzed by PCA, FEL, DCCM and MM/PBSA.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental and molecular dynamics investigation of ZnO nanoparticle size effects on sunscreen performance and skin-lipid interactions","authors":"Nigar Kantarci-Carsibasi,&nbsp;Melis Ersoy,&nbsp;Rana Tosun,&nbsp;Shirin Tarbiat","doi":"10.1007/s00894-026-06954-7","DOIUrl":"10.1007/s00894-026-06954-7","url":null,"abstract":"<div><h3>Context</h3><p>Zinc oxide (ZnO) nanoparticles are widely used as inorganic UV filters in sunscreen formulations; however, particle size can influence photoprotective efficacy, formulation stability, cosmetic properties, and interactions with the skin barrier. This study experimentally investigated the effect of ZnO nanoparticle size on sunscreen performance and complemented these findings with molecular dynamics (MD) simulations to characterize ZnO-stratum corneum (SC) interactions at the molecular level. SPF increased from 1.24 in the ZnO-free control to 2.61 and 3.23 in formulations containing 18 nm and 30–50 nm ZnO nanoparticles, respectively. Despite its higher SPF, the 30–50 nm formulation exhibited phase separation, increased pH, and pronounced whitening after skin application, whereas the 18 nm formulation showed a more balanced physical stability, skin-compatible pH, and cosmetic performance. MD simulations further demonstrated that both crystal-derived ZnO and a 1 nm ZnO nanoparticle remained preferentially localized at the SC lipid interface without evidence of deeper penetration. Persistently negative ZnO-SC interaction energies, together with density-depth and spatial projection analyses, supported sustained association and interfacial retention of ZnO within the SC lipid environment, with no deeper penetration observed within the 100 ns simulation timescale. Overall, the 18 nm ZnO formulation provided the most favorable balance between photoprotection, formulation stability, skin compatibility, and cosmetic acceptability, while the computational findings provided molecular-level support for the interfacial retention of ZnO within the SC lipid matrix.</p><h3>Methods</h3><p>Three sunscreen formulations were prepared: a ZnO-free control and formulations containing 5% (w/w) ZnO nanoparticles with particle sizes of 18 nm or 30–50 nm. The formulations were characterized by in vitro sun protection factor (SPF), pH, physical stability, and skin-application assessments. To investigate ZnO-skin interactions at the molecular level, 100 ns all-atom MD simulations were performed using a representative SC lipid model composed of ceramides, cholesterol, and free fatty acids. Two complementary ZnO representations, a crystal-derived ZnO model and a computationally tractable 1 nm ZnO nanoparticle model, were evaluated. ZnO localization and retention within the lipid matrix were characterized using interaction-energy profiles, trajectory-density analysis, density-depth distributions, and spatial projection analyses.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms of thermo-oxidative stabilization in antioxidant-modified polyisoprene: bridging DFT calculations with macroscopic performance","authors":"Enasty Pratiwi Wulandari,&nbsp;Muhammad Faizal,&nbsp;Tuti Indah Sari,&nbsp;Nukman Nukman","doi":"10.1007/s00894-026-06917-y","DOIUrl":"10.1007/s00894-026-06917-y","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;Thermo-oxidative and ozone-induced degradation of natural rubber (NR) in modified asphalt necessitates the use of robust antidegradants, yet the precise quantum–mechanical prediction mechanisms underlying their action remain largely unexplored. This study integrates macroscopic experimental characterizations with density functional theory (DFT) simulations to evaluate the competitive efficacies and thermodynamic profiles of 6PPD, TMQ, and BHT. Theoretical evaluation reveals that hydrogen atom transfer (HAT) exclusively dominates radical scavenging, where the endergonic nature of TMQ (Δ&lt;i&gt;G&lt;/i&gt;&lt;sub&gt;rxn&lt;/sub&gt; = + 1.4 kcal/mol) establishes it as a superior high-temperature thermodynamic reservoir, experimentally yielding a 99.2% tensile retention post-aging. Conversely, BHT suffers from rapid depletion due to its highly spontaneous dissociation (BDE = 74.0 kcal/mol). Transition state analyses provide a robust theoretical kinetic rationale for the antiozonant superiority of 6PPD; its simultaneous hydrogen abstraction of ozone requires a remarkably low activation barrier (Δ&lt;i&gt;G&lt;/i&gt;&lt;sup&gt;‡&lt;/sup&gt; = + 3.9 kcal/mol), successfully outcompeting the concerted cycloaddition required to cleave the polyisoprene backbone (Δ&lt;i&gt;G&lt;/i&gt;&lt;sup&gt;‡&lt;/sup&gt; = + 10.2 kcal/mol). The irreversible oxidative transformation of 6PPD into a quinone derivative was theoretically mapped, yielding a computed asymmetric C = O stretching fingerprint at 1700.6 cm&lt;sup&gt;−1&lt;/sup&gt;, which provides a precise spectroscopic target for its trace identification. Additionally, the drastic curing acceleration induced by 6PPD (&lt;i&gt;t&lt;/i&gt;&lt;sub&gt;&lt;i&gt;s&lt;/i&gt;2&lt;/sub&gt; = 1:44 min) is fundamentally rationalized by its exceptional binding affinity toward the Zn&lt;sup&gt;2+&lt;/sup&gt; activator (Δ&lt;i&gt;G&lt;/i&gt;&lt;sub&gt;bind&lt;/sub&gt; = − 275.2 kcal/mol). This synergistic approach robustly bridges coordination thermodynamics and transition-state kinetics with empirical macroscopic stability.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;All quantum chemical calculations were performed using density functional theory (DFT) at the B3LYP-D3(BJ)/def2-TZVP level of theory. The ORCA 6.1.1 software package was employed for all computational modeling, conducted in the gas phase under standard conditions (298.15 K, 1 atm) with unscaled zero-point energy (ZPE) corrections applied. Intrinsic molecular reactivities were extracted via conceptual DFT (CDFT) using frontier molecular orbital (FMO) energies. Transition-state (TS) geometries were approximated using relaxed surface scans (RSS) and subsequently subjected to rigorous saddle-point optimizations (OptTS), with authenticity verified by the presence of a single imaginary frequency in harmonic vibrational analysis. Theoretical infrared (IR) spectra were simulated via analytical frequency calculations. Experimentally, formulated NR compounds (F1–F4) were prepared via a two-roll open mill and vulcanized at 150 °C. Accelerated thermal aging was conducted in an air-circulating oven at 100 °C for 72 h. Macrosco","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148986924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into reaction mechanisms and kinetic characteristics of electron-beam irradiation-induced decomposition of 2,3,7,8-TCDD: a ReaxFF-based MD simulation study","authors":"Huiwen Hu,&nbsp;Jiaxin Feng,&nbsp;Qiulin Wang,&nbsp;Yaqi Peng,&nbsp;Shengyong Lu,&nbsp;Minghui Tang,&nbsp;Dunyu Liu,&nbsp;Jing Jin","doi":"10.1007/s00894-026-06957-4","DOIUrl":"10.1007/s00894-026-06957-4","url":null,"abstract":"<div><h3>Objective</h3><p>Recognized by the International Atomic Energy Agency (IAEA) as a pivotal technology for the peaceful use of nuclear energy, electron beam (EB) irradiation holds significant potential for degrading persistent organic pollutants, such as polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). However, the atomistic reaction mechanisms involved in this process remain inadequately understood, impeding the rational optimization and practical application of the technology.</p><h3>Methods</h3><p>To address this knowledge gap, molecular dynamics (MD) simulations using reactive force field (ReaxFF-based MD simulation) were employed to investigate the EB-induced decomposition of 2,3,7,8-tetrachlorodibenzo-<i>p</i>-dioxin (2,3,7,8-TCDD) over a wide temperature range of 1000–3000 K.</p><h3>Results</h3><p>The simulations reveal that hydroxyl radicals (·OH) exhibit the highest reactivity among the key reactive species (·OH, O and O₃) generated in EB irradiation. At 3000 K and ER=1 (defined as the stoichiometric ratio of ROS to 2,3,7,8-TCDD), the decomposition rate of 2,3,7,8-TCDD in the presence of ·OH is enhanced by factors of 2.0 and 4.3 compared to O and O₃, respectively. Temperature is also shown to critically influence both the reaction pathways and product distribution. At 1000 K, 2,3,7,8-TCDD initially undergoes polymerization prior to fragmentation, while direct dechlorination and ring-opening prevail at 2000 K and 3000 K. Correspondingly, increasing the temperature from 1000 K to 3000 K reduces the time required for the complete decomposition of 2,3,7,8-TCDD by an order of magnitude, elevates the CO₂ selectivity from 13% to 95% and also shifts the dominant chlorine-containing product from HClO to HCl. Furthermore, a stepwise degradation pathway of 2,3,7,8-TCDD initiated by <b>·</b>OH is proposed based on the simulation trajectories, involving sequential dechlorination, ring cleavage and ultimate mineralization. The kinetic analysis shows that the reaction follows 1st-order dependence on 2,3,7,8-TCDD and 0.32-order dependence on ·OH, with an apparent activation energy of 28.70 ± 0.3 kJ·mol⁻¹ and a pre-exponential factor of (4.72 ± 0.5) × 10¹² mol·L⁻¹·s⁻¹.</p><h3>Conclusions</h3><p>Overall, this work provides fundamental insights into the reaction mechanisms and kinetics governing the EB-induced degradation of 2,3,7,8-TCDD, offering a theoretical basis for the advanced application of EB technology in environmental remediation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Substituent-controlled electronic redistribution and nonlinear optical response across the Ag-S interface in W@Ag12 -BDT hybrids: a DFT/TD-DFT study","authors":"Tran Huynh Hoang Loc,&nbsp;Minh Triet Dang,&nbsp;Dang T. Nguyen,&nbsp;Pham Vu Nhat","doi":"10.1007/s00894-026-06952-9","DOIUrl":"10.1007/s00894-026-06952-9","url":null,"abstract":"<div><h3>Context</h3><p>Atomically precise silver nanoclusters provide well-defined inorganic platforms for molecular modeling of cluster-π interactions, but the relationships among terminal substitution, electronic redistribution across an Ag–S anchoring environment, and molecular nonlinear optical response remain insufficiently understood. Herein, W@Ag₁₂-BDT-X hybrids, where BDT denotes benzo[1,2-b:4,5-b′]dithiophene and X = H, CH₃, NH₂, SCH₃, NO₂, CN, and CF₃, are examined as a structurally comparable molecular series. The optimized complexes retain the W-centered Ag₁₂ framework, while the selected structural parameters show only limited variation, with W-Ag distances ranging from approximately 2.70 to 2.73 Å, an Ag-S_anchor distance of approximately 2.53 Å, and a neighboring Ag–Ag distance of approximately 2.86 Å. This structural comparability supports interpretation of the observed property trends in relation to substituent-dependent electronic redistribution, while smaller geometric contributions cannot be excluded. Within the investigated series, donor substitution is associated with increased interfacial polarization, whereas acceptor substitution is associated more clearly with LUMO stabilization and increased ligand participation in selected excited states. C-NH₂ gives the largest first hyperpolarizability in the series, with β_tot values of 7036.3, 8044.8, and 10,849.2 a.u. at 0, −ω, and −2ω, respectively; by contrast, the second hyperpolarizability is more sensitive to frequency, functional choice, and projected tensor contributions.</p><h3>Methods</h3><p>Geometry optimization, frequency analysis, frontier-orbital analysis, time-dependent density functional theory (TD-DFT) calculations, and static/dynamic NLO computations were performed using Gaussian 16. The long-range-corrected LC-BLYP functional was employed with aug-cc-pVDZ for non-metal atoms and aug-cc-pVDZ-PP effective-core-potential basis sets for Ag and W atoms. Hole-electron descriptors and orbital contributions were analyzed using Multiwfn, while frontier orbitals, hole-electron distributions, and density-difference maps were visualized using VESTA. Dynamic NLO responses were evaluated at 1064 nm.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Triazolo-triazine derivatives outperforming CL-20: computational discovery and substituent engineering for superior energetic materials","authors":"Yang Zhu,&nbsp;Yiming Liu,&nbsp;Peng Ma,&nbsp;Congming Ma","doi":"10.1007/s00894-026-06922-1","DOIUrl":"10.1007/s00894-026-06922-1","url":null,"abstract":"<div><h3>Context</h3><p>Triazolo[4,5-d]triazine fused-ring energetic materials exhibit excellent thermal stability and low mechanical sensitivity, but their detonation performance is generally inferior to CL-20. To overcome this limitation, this study utilizes the nitrogen-rich triazolo[4,5-d]triazine fused-ring system as a parent scaffold. By incorporating energetic functional groups—including azido, trinitromethyl, hydrazino, nitro, nitramino, cyano, nitrate ester, and dinitromethyl moieties—we designed 64 novel energetic derivatives across four distinct series (A–D). Furthermore, we systematically investigated the substituent effects on molecular energy, crystal packing, detonation performance, impact sensitivity, and electronic structure, aiming to screen for high-performance energetic candidates. Of the 64 derivatives designed, compounds D6, B8, B6, and D14 demonstrate superior performance with detonation velocities over 9.5 km/s and detonation pressures exceeding 43 GPa, surpassing RDX and HMX and nearing the performance of the benchmark explosive CL-20. D6 (<i>D</i> = 9.68 km/s, <i>P</i> = 43.82 GPa) stands out with superior detonation performance, whereas B6 exhibits the greatest crystal density at 2.0021 g·cm⁻³. These four candidates warrant priority for future experimental synthesis and evaluation.</p><h3>Methods</h3><p>Quantum chemical, crystal prediction, and detonation simulations were carried out at the M06-2X/6-311G(d,p) level using Gaussian 16, Materials Studio, and Multiwfn.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 10","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}